Linked Life Data

10637326

Source:http://linkedlifedata.com/resource/pubmed/id/10637326

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2000-3-6
pubmed:abstractText
The performance of computational tools that can predict human splice sites are reviewed using a test set of EST-confirmed splice sites. The programs (namely HMMgene, NetGene2, HSPL, NNSPLICE, SpliceView and GeneID-3) differ from one another in the degree of discriminatory information used for prediction. The results indicate that, as expected, HMMgene and NetGene2 (which use global as well as local coding information and splice signals) followed by HSPL (which uses local coding information and splice signals) performed better than the other three programs (which use only splice signals). For the former three programs, one in every three false positive splice sites was predicted in the vicinity of true splice sites while only one in every 12 was expected to occur in such a region by chance. The persistence of this observation for programs (namely FEXH, GRAIL2, MZEF, GeneID-3, HMMgene and GENSCAN) that can predict all the potential exons (including optimal and sub-optimal) was assessed. In a high proportion (>50%) of the partially correct predicted exons, the incorrect exon ends were located in the vicinity of the real splice sites. Analysis of the distribution of proximal false positives indicated that the splice signals used by the algorithms are not strong enough to discriminate particularly those false predictions that occur within +/- 25 nt around the real sites. It is therefore suggested that specialised statistics that can discriminate real splice sites from proximal false positives be incorporated in gene prediction programs.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-10373578, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-10454621, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-1619647, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-1763041, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-2067018, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-7731036, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-7816600, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-8786136, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-9012824, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-9149143, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-9211734, http://linkedlifedata.com/resource/pubmed/commentcorrection/10637326-9666331
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Feb
pubmed:issn
1362-4962
pubmed:author
pubmed:issnType
Electronic
pubmed:day
1
pubmed:volume
28
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
744-54
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2000
pubmed:articleTitle
Positional characterisation of false positives from computational prediction of human splice sites.
pubmed:affiliation
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. thanaraj@ebi.ac.uk
pubmed:publicationType
Journal Article, Comparative Study